Tumor suppressor p53 induces apoptosis through the transactivation of target genes. Previous work has shown that p53-dependent gene expression changes in response to ionizing radiation are tissue specific. To determine critical p53 target genes in the colon, we irradiated wild-type and p53-null mice and examined the global p53 gene expression patterns in response to ionizing radiation. Microarray analysis using the Affymetrix MOE430A genechip showed that many of the genes that increased in a p53-dependent manner are serine proteases (e.g., elastase, trypsin) and other proteases (e.g., carboxypeptidases). Reverse transcription polymerase chain reaction (RT-PCR), immunohistochemistry, and Western blots were used to validate microarray results on trypsin 4, carboxypeptidase A1, and elastase-2, three genes that have potential p53-binding elements. Further study of tissue specific mediators of p53-dependent responses such as serine proteases will greatly increase understanding of in vivo p53-dependent pathways within the colon triggered by ionizing radiation.